Genetic loci and causal genes for seed fatty acids accumulation across multiple environments and genetic backgrounds in soybean

Li, Xihuan; Tian, Rui; Shao, Zhenqi; Zhang, Hua; Chu, Jiahao; Li, Wenlong; Kong, Youbin; Du, Hui; Zhang, Caiying

doi:10.1007/s11032-021-01227-y

Cited by 5 publications

(3 citation statements)

References 37 publications

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“…Soybean fatty acid components exhibit specific correlations in their relative content [43,44]. However, the generated correlations vary depending on the ecological environment, quantity, and sources of the studied varieties [45].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Analysis-Based Mining of Quality Genes Related to Linoleic and Linolenic Acids in Soybean

Wang,

Liu,

Zhang

et al. 2023

Agriculture

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Soybean fat contains five principal fatty acids, and its fatty acid composition and nutritional value depend on the type of soybean oil, storage duration, and conditions. Among the fat contents, polyunsaturated fatty acids, such as linoleic acid and linolenic acid, play an essential role in maintaining human life activities; thus, increasing the proportions of the linoleic acid and linolenic acid contents can help improve the nutritional value of soybean oil. Our laboratory completed SLAF-seq whole genome sequencing of the natural population (292 soybean varieties) in the previous growth period. In this study, genome-wide association analysis (GWAS) was performed based on the natural population genotypic data and three-year phenotypic data of soybean linoleic acid and linolenic acid contents, and a significant single nucleotide polymorphisms (SNPs) locus (Gm13_10009679) associated with soybean oleic acid content was repeatedly detected over a span of 3 years using the GLM model and MLM model. Additionally, another significant SNP locus (Gm19_41366844) correlated with soybean linolenic acid was identified through the same models. Genes within the 100 Kb interval upstream and downstream of the SNP loci were scanned and analyzed for their functional annotation and enrichment, and one gene related to soybean linoleic acid synthesis (Glyma.13G035600) and one gene related to linolenic acid synthesis (Glyma.19G147400) were screened. The expressions of the candidate genes were verified using qRT-PCR, and based on the verification results, it was hypothesized that Glyma.13G035600 and Glyma.19G147400 positively regulate linoleic acid and linolenic acid synthesis and accumulation, respectively. The above study lays the foundation for further validating gene functions, and analyzing the regulatory mechanisms of linoleic acid and linolenic acid synthesis and accumulation in soybean.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Analysis-Based Mining of Quality Genes Related to Linoleic and Linolenic Acids in Soybean

Wang,

Liu,

Zhang

et al. 2023

Agriculture

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“…Fatty acids [173] HPLC-DAD Isoflavones [174] HPLC-MS Aminoacids, isoflavones, lipids, organic acids [175] Tea Camellia sinensis L. HPLC Theanine, caffeine, catechins [176] HPLC-PDA Amino acids, caffeine, catechins [177] Tomato S. lycopersicum GC-MS Organic acids, sugars [178] GC-MS Amino acids, organic acid ‡ ‡ , sugars [179] HPLC-MS/MS Alkaloids ‡ ‡ ‡ [180] GC-MS Fatty acids, lipids, carotenoids (i.e., tocopherols and tocotrienols: vitamin E) [181] Wheat T. aestivum HPLC-ESI-QTRAP-MS/MS Amino acids, (poly)amines, flavonoids, organic acids, sugars, vitamins, etc.…”

Section: Gcmentioning

confidence: 99%

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

Medina-Lozano

Díaz

2022

IJMS

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Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.

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“…In addition to the known variants described above, studies have identified numerous additional QTL that impact oil content in soybean (Li et al., 2021; Silva et al., 2021; Sung et al., 2021; Yao et al., 2020). This suggests that there remains a significant degree of untapped genetic potential for modification of this trait.…”

Section: Introductionmentioning

confidence: 99%

Diversity of fatty acid biosynthesis genes across the soybean pangenome

et al. 2023

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Soybean (Glycine max) is a major crop that contributes more than half of global oilseed production. Much research has been directed towards improvement of the fatty acid profile of soybean seeds through marker assisted breeding. Recently published soybean pangenomes, based on thousands of soybean lines, provide an opportunity to identify new alleles that may be involved in fatty acid biosynthesis. In this study, we identify fatty acid biosynthesis genes in soybean pangenomes based on sequence identity with known genes and examine their sequence diversity across diverse soybean collections. We find three possible instances of a gene missing in wild soybean, including FAD8 and FAD2-2D, which may be involved in oleic and linoleic acid desaturation, respectively, although we recommend follow-up research to verify the absence of these genes. More than half of the 53 fatty acid biosynthesis genes identified contained missense variants, including one linked with a previously identified QTL for oil quality. These variants were present in multiple studies based on either short read mappings or alignment of reference grade genomes. Missense variants were found in previously characterized genes including FAD2-1A and FAD2-1B, both of which are involved in desaturation of oleic acid, as well as uncharacterized candidate fatty acid biosynthesis genes. We find that the frequency of missense alleles in fatty acid biosynthesis genes has been reduced significantly more than the global average frequency of missense mutations during domestication, and missense variation in some genes is near absent in modern cultivars. This could be due to the selection for fatty acid profiles in seed, though future work should be conducted towards understanding the phenotypic impacts of these variants.

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Genetic loci and causal genes for seed fatty acids accumulation across multiple environments and genetic backgrounds in soybean

Cited by 5 publications

References 37 publications

Genome-Wide Association Analysis-Based Mining of Quality Genes Related to Linoleic and Linolenic Acids in Soybean

Genome-Wide Association Analysis-Based Mining of Quality Genes Related to Linoleic and Linolenic Acids in Soybean

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

Diversity of fatty acid biosynthesis genes across the soybean pangenome

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